cpld_control_run.IN

mkdir INPUT RESTART

mkdir -p $CICE_RESTART_DIR
mkdir -p $MOM6_RESTART_DIR
mkdir -p $CMEPS_RESTART_DIR

mkdir -p $CICE_HISTORY_DIR
mkdir -p $MOM6_OUTPUT_DIR

if [[ $ATMRES == C96 ]]; then
    FV3_DIR=FV3_input_data
else
    FV3_DIR=FV3_input_data${ATMRES#C}
fi

if [[ $ATMRES == C24 ]] || [[ $ATMRES == C12 ]]; then
    LEVELS=L41
else
    LEVELS=L127
fi

ICERES=${OCNRES:0:1}.${OCNRES:1}

V2_SFC_FILE=${V2_SFC_FILE:-false}

# IC input directories
if [[ ${BMIC} == .true. ]]; then
    FV3_IC=@[INPUTDATA_ROOT]/GEFS/${SYEAR}${SMONTH}${SDAY}${SHOUR}
    MOM_IC=${FV3_IC}; ICE_IC=${FV3_IC}; WAV_IC=${FV3_IC};
elif [[ $ULTRALOW == .true. ]]; then
    FV3_IC=@[INPUTDATA_ROOT]/${FV3_DIR}/INPUT_${LEVELS}_mx${OCNRES}/${SYEAR}${SMONTH}${SDAY}${SHOUR}
    MOM_IC=@[INPUTDATA_ROOT]/MOM6_IC/${ATMRES}mx${OCNRES}/${SYEAR}${SMONTH}${SDAY}${SHOUR}
    ICE_IC=@[INPUTDATA_ROOT]/CICE_IC/${ATMRES}mx${OCNRES}/${SYEAR}${SMONTH}${SDAY}${SHOUR}
elif [[ $GFSv17opn == .true. ]]; then
    FV3_IC=@[INPUTDATA_GFSv17opn]/FV3_IC
    MOM_IC=@[INPUTDATA_GFSv17opn]/MOM6_IC
    ICE_IC=@[INPUTDATA_GFSv17opn]/CICE_IC
    WAV_IC=@[INPUTDATA_GFSv17opn]/WW3_IC
    CMEPS_IC=@[INPUTDATA_GFSv17opn]/CMEPS_IC
elif [[ $SFS == .true. ]]; then
    FV3_IC=@[INPUTDATA_ROOT]/SFS/${SYEAR}${SMONTH}${SDAY}${SHOUR}
    MOM_IC=${FV3_IC}
    ICE_IC=${FV3_IC}
else
    if [ "$V2_SFC_FILE" = "true" ]; then
        FV3_IC=@[INPUTDATA_ROOT]/${FV3_DIR}/INPUT_L127_mx${OCNRES}_v2_sfc
    else
        FV3_IC=@[INPUTDATA_ROOT]/${FV3_DIR}/INPUT_L127_mx${OCNRES}
    fi
    MOM_IC=@[INPUTDATA_ROOT]/MOM6_IC
    ICE_IC=@[INPUTDATA_ROOT]/CICE_IC
fi

# FV3 fixed input
if [[ $GFSv17opn == .true. ]]; then
    cp @[INPUTDATA_GFSv17opn]/FV3_fix/*.nc ./INPUT
    cp @[INPUTDATA_GFSv17opn]/FV3_fix/*.grb .
    cp @[INPUTDATA_GFSv17opn]/FV3_fix_tiled/* .
    cp @[INPUTDATA_GFSv17opn]/MOM6_FIX/* ./INPUT
    cp @[INPUTDATA_GFSv17opn]/CICE_FIX/* .
    cp @[INPUTDATA_GFSv17opn]/WW3_FIX/@[WW3_MODDEF] mod_def.ww3
    # TODO: when uglo_15km is present in standard input-data location
    # replace the above line with the following location for the mod_def.ww3
    # the existing mod_def in the GFSv17opn/WW3_FIX directory should be removed
    # cp @[INPUTDATA_ROOT_WW3]/@[WW3_MODDEF] mod_def.ww3

    cp @[INPUTDATA_GFSv17opn]/WW3_FIX/@[MESH_WAV] .
    cp @[INPUTDATA_GFSv17opn]/WW3_FIX/wave_gfs.buoys.full ww3_points.list
    cp @[INPUTDATA_GFSv17opn]/WW3_FIX/pnt_wght.uglo_15km.nc pnt_wght.ww3.nc
    cp @[INPUTDATA_GFSv17opn]/WW3_FIX/ww3_shel.nml .
else
    cp @[INPUTDATA_ROOT]/${FV3_DIR}/@[FNSMCC] .
    cp @[INPUTDATA_ROOT]/${FV3_DIR}/@[FNMSKH] .
    cp @[INPUTDATA_ROOT]/FV3_fix/@[FNGLAC] .
    cp @[INPUTDATA_ROOT]/FV3_fix/@[FNMXIC] .
    cp @[INPUTDATA_ROOT]/FV3_fix/@[FNTSFC] .
    cp @[INPUTDATA_ROOT]/FV3_fix/@[FNSNOC] .
    cp @[INPUTDATA_ROOT]/FV3_fix/@[FNAISC] .

    cp @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]mx@[OCNRES]/oro_@[ATMRES].mx@[OCNRES].tile1.nc INPUT/oro_data.tile1.nc
    cp @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]mx@[OCNRES]/oro_@[ATMRES].mx@[OCNRES].tile2.nc INPUT/oro_data.tile2.nc
    cp @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]mx@[OCNRES]/oro_@[ATMRES].mx@[OCNRES].tile3.nc INPUT/oro_data.tile3.nc
    cp @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]mx@[OCNRES]/oro_@[ATMRES].mx@[OCNRES].tile4.nc INPUT/oro_data.tile4.nc
    cp @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]mx@[OCNRES]/oro_@[ATMRES].mx@[OCNRES].tile5.nc INPUT/oro_data.tile5.nc
    cp @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]mx@[OCNRES]/oro_@[ATMRES].mx@[OCNRES].tile6.nc INPUT/oro_data.tile6.nc
    cp @[INPUTDATA_ROOT]/FV3_fix_tiled/@[ATMRES]mx@[OCNRES]/@[ATMRES]*.nc .

    cp @[INPUTDATA_ROOT]/CPL_FIX/a@[ATMRES]o@[OCNRES]/grid_spec.nc ./INPUT
    cp @[INPUTDATA_ROOT]/${FV3_DIR}/INPUT/@[ATMRES]_grid*.nc ./INPUT
    cp @[INPUTDATA_ROOT]/${FV3_DIR}/INPUT/grid_spec.nc ./INPUT/@[ATMRES]_mosaic.nc

    # MOM6 fixed input
    cp @[INPUTDATA_ROOT]/MOM6_FIX/@[OCNRES]/* ./INPUT

    # CICE fixed input
    cp @[INPUTDATA_ROOT]/CICE_FIX/@[OCNRES]/grid_cice_NEMS_mx@[OCNRES].nc .
    cp @[INPUTDATA_ROOT]/CICE_FIX/@[OCNRES]/kmtu_cice_NEMS_mx@[OCNRES].nc .
    cp @[INPUTDATA_ROOT]/CICE_FIX/@[OCNRES]/mesh.mx@[OCNRES].nc .

    # WW3 fix/input
    if [[ $CPLWAV == .true. ]]; then
        cp @[INPUTDATA_ROOT_WW3]/@[WW3_MODDEF] mod_def.ww3
        if [[ ${WW3_DOMAIN:0:2} != mx ]]; then
            cp @[INPUTDATA_ROOT_WW3]/@[MESH_WAV] .
        fi
    fi
fi

#rrtmgp
if [ $DO_RRTMGP = .true. ]; then
    cp @[INPUTDATA_ROOT]/FV3_input_data_RRTMGP/* .
fi

# 1993,94,95 co2 for SFS
if [[ $SFS == .true. ]]; then
    cp ${FV3_IC}/co2historicaldata* ./.
    cp ${FV3_IC}/ozprdlos_2015_new_sbuvO3_tclm15_nuchem_shozhvlogp.f77 ./global_o3prdlos.f77
fi

OPNREQ_TEST=${OPNREQ_TEST:-false}
SUFFIX=${RT_SUFFIX}
# No restart
if [[ $WARM_START == .false. ]]; then
    # ICs
    cp ${FV3_IC}/sfc_data*.nc ./INPUT
    cp ${FV3_IC}/gfs_data*.nc ./INPUT
    cp ${FV3_IC}/gfs_ctrl.nc ./INPUT
    if [[ $ULTRALOW == .true. ]]; then
        cp ${MOM_IC}/MOM.res.nc ./INPUT
        cp ${ICE_IC}/* ./cice_model.res.nc
    elif [[ $OCNICE_WARMSTART == .true. ]]; then
        cp ${MOM_IC}/mom6.mx@[OCNRES].${SYEAR}${SMONTH}${SDAY}${SHOUR}.warmstart.nc ./INPUT/mom6.warmstart.nc
        cp ${ICE_IC}/cice.mx@[OCNRES].${SYEAR}${SMONTH}${SDAY}${SHOUR}.warmstart.nc ./cice.warmstart.nc
    else
        cp ${MOM_IC}/MOM6_IC_TS_${SYEAR}${SMONTH}${SDAY}${SHOUR}.nc ./INPUT/MOM6_IC_TS.nc
        cp ${ICE_IC}/${OCNRES}/cice_model_@[ICERES].cpc.res_${SYEAR}${SMONTH}${SDAY}.nc ./cice_model.res.nc
    fi
    if [[ $SFS == .true. ]]; then
        cp ${FV3_IC}/atminc.nc ./INPUT/.
        cp ${MOM_IC}/mom6_increment.nc ./INPUT/.
    fi
else
#Restart from checkpoint restart
    if [[ "Q${DEP_RUN:-}" != Q ]] ; then
        if [[ ${OPNREQ_TEST} == true ]]; then
            SUFFIX=${BL_SUFFIX}
        fi

        # Restart files
        cp -r ../${DEP_RUN}${SUFFIX}/INPUT/* ./INPUT
        cp -r ../${DEP_RUN}${SUFFIX}/RESTART/${RESTART_FILE_PREFIX}.* ./INPUT
        for RFILE in INPUT/${RESTART_FILE_PREFIX}.*; do
            [ -e $RFILE ] || exit 1
            RFILE_OLD=$(basename $RFILE)
            mv -f $RFILE INPUT/"${RFILE_OLD//${RESTART_FILE_PREFIX}./}"
        done
        if [[ $IAU_OFFSET == 6 ]] && [[ $FHROT -le 6 ]]; then
            cp @[INPUTDATA_ROOT]/${FV3_DIR}/INPUT_L127_mx${OCNRES}/fv_increment*.nc ./INPUT/.
        fi

        #if not mx025, then mom6 restart is a single file
        if [[ $OCNRES == 025 ]]; then
            cp ../${DEP_RUN}${SUFFIX}/${MOM6_RESTART_DIR}/${RESTART_FILE_PREFIX}.MOM.res.nc ./INPUT/MOM.res.nc
            cp ../${DEP_RUN}${SUFFIX}/${MOM6_RESTART_DIR}/${RESTART_FILE_PREFIX}.MOM.res_1.nc ./INPUT/MOM.res_1.nc
            cp ../${DEP_RUN}${SUFFIX}/${MOM6_RESTART_DIR}/${RESTART_FILE_PREFIX}.MOM.res_2.nc ./INPUT/MOM.res_2.nc
            cp ../${DEP_RUN}${SUFFIX}/${MOM6_RESTART_DIR}/${RESTART_FILE_PREFIX}.MOM.res_3.nc ./INPUT/MOM.res_3.nc
        else
            cp ../${DEP_RUN}${SUFFIX}/${MOM6_RESTART_DIR}/${RESTART_FILE_PREFIX}.MOM.res.nc ./INPUT/MOM.res.nc
            if [[ $ODA_INCUPD == 'True' ]] && [[ $FHROT -le 6 ]]; then
                if [[ ${BMIC} ]]; then
                    cp ${MOM_IC}/mom6_increment.nc ./INPUT
                else
                    cp @[INPUTDATA_ROOT]/MOM6_IC/mom6_increment.nc ./INPUT/mom6_increment.nc
                fi
            fi
        fi

        # CMEPS restart and pointer files
        RFILE=ufs.cpld.cpl.r.${RESTART_FILE_SUFFIX_SECS}.nc
        cp  ../${DEP_RUN}${SUFFIX}/${CMEPS_RESTART_DIR}/${RFILE} .
        ls -1 ${RFILE}>rpointer.cpl

        # CMEPS/CCPP restart file
        if [[ $CPLMODE =~ 'ufs.frac.aoflux' ]]; then
            RFILE_CCPP=ufs.cpld.cpl.ccpp.${RESTART_FILE_SUFFIX_SECS}.nc
            cp ../${DEP_RUN}${SUFFIX}/${RFILE_CCPP} .
        fi

        # CICE restart and pointer files
        RFILE=iced.${RESTART_FILE_SUFFIX_SECS}.nc
        cp  ../${DEP_RUN}${SUFFIX}/${CICE_RESTART_DIR}/${RFILE} ./INPUT
        ls -1 ./INPUT/${RFILE}>ice.restart_file

        # WAVE restart file
        if [[ $CPLWAV == .true. ]]; then
            RFILE=ufs.cpld.ww3.r.${RESTART_FILE_SUFFIX_SECS}.nc
            cp ../${DEP_RUN}${SUFFIX}/${RFILE} .
            if [[ $WW3_DOMAIN == 'global_270k' ]]; then
                if [[ -f ../${DEP_RUN}${SUFFIX}/out.pnt_wght.ww3.nc ]]; then
                    cp ../${DEP_RUN}${SUFFIX}/out.pnt_wght.ww3.nc pnt_wght.ww3.nc
                else
                    cp ../${DEP_RUN}${SUFFIX}/pnt_wght.ww3.nc pnt_wght.ww3.nc
                fi
            fi
        fi

        # LAND restart file
        if [ $CPLLND = .true. ]; then
            cp ../${DEP_RUN}${SUFFIX}/ufs.cpld.lnd.out.${RESTART_FILE_SUFFIX_SECS}.tile*.nc RESTART/.
        fi

        # FV3 route handle files
        if [[ $USE_FV3_ROUTEHANDLES = .true. ]]; then
            cp ../${DEP_RUN}${SUFFIX}/routehandle_fb* ./
        fi

    elif [[ $ULTRALOW == .true. ]]; then
        # Warm starts from ICs; all cases use 9km unstructured WW3
        cp ${FV3_IC}/*.nc ./INPUT
        cp ${MOM_IC}/MOM.res.nc ./INPUT
        cp ${ICE_IC}/iced* ./INPUT
        cp ${ICE_IC}/ice.restart_file .
        cp @[INPUTDATA_ROOT]/CMEPS_IC/${ATMRES}mx${OCNRES}/${SYEAR}${SMONTH}${SDAY}${SHOUR}/* .
        cp @[INPUTDATA_ROOT]/WW3_IC/${ATMRES}mx${OCNRES}/${SYEAR}${SMONTH}${SDAY}${SHOUR}/* .
    elif [[ ${BMIC} == .true. ]]; then
        cp ${FV3_IC}/fv*.nc ./INPUT
        cp ${FV3_IC}/sfc_data*.nc ./INPUT
        cp ${FV3_IC}/phy_data*.nc ./INPUT
        cp ${MOM_IC}/MOM*.nc ./INPUT
        cp ${MOM_IC}/mom6_increment.nc ./INPUT
        cp ${MOM_IC}/interpolate_zgrid_26L.nc ./INPUT
        cp ${ICE_IC}/cice*nc ./INPUT
        ls -1 ./INPUT/cice*nc>ice.restart_file
        cp ${FV3_IC}/*stoch*nc ./INPUT
        cp ${FV3_IC}/ca_data*nc ./INPUT
        cp ${FV3_IC}/ufs.cpld.cpl*nc .
        ls -1 ufs.cpld.cpl*nc>rpointer.cpl
        cp ${WAV_IC}/ufs.cpld.ww3.r.${RESTART_FILE_SUFFIX_SECS}.nc .
    elif [[ $GFSv17opn == .true. ]]; then
        cp ${FV3_IC}/* ./INPUT
        cp ${MOM_IC}/* ./INPUT
        cp  ${ICE_IC}/iced.* ./cice_model.res.nc
        ls -1 cice_model.res.nc>ice.restart_file
        cp ${WAV_IC}/* .
        cp ${CMEPS_IC}/ufs.cpld.cpl.r* ufs.cpld.cpl.r.nc
        ls -1 ufs.cpld.cpl.r.nc>rpointer.cpl
    fi
fi

#inline post
if [ $WRITE_DOPOST = .true. ]; then
  if [[ ${BMIC} == .true. ]]; then
    cp    ${PATHRT}/../UFSATM/upp/parm/gefs/post_itag_gefs128 itag
    cp    ${PATHRT}/../UFSATM/upp/parm/gefs/postxconfig-NT-gefs.txt postxconfig-NT.txt
    cp    ${PATHRT}/../UFSATM/upp/parm/gefs/postxconfig-NT-gefs-f00.txt postxconfig-NT_FH00.txt
    cp    ${PATHRT}/../UFSATM/upp/parm/params_grib2_tbl_new params_grib2_tbl_new
    cp    ${PATHRT}/../UFSATM/upp/fix/chem/optics_luts*nasa.dat .
  else
    cp    ${PATHRT}/parm/post_itag_gfs itag
    cp    ${PATHRT}/parm/postxconfig-NT-gfs.txt postxconfig-NT.txt
    cp    ${PATHRT}/parm/postxconfig-NT-gfs_FH00.txt postxconfig-NT_FH00.txt
    cp    ${PATHRT}/../UFSATM/upp/parm/params_grib2_tbl_new params_grib2_tbl_new
  fi
fi

#prognostic aerosols
if [ $CPLCHM = .true. ]; then
    if [[ ${BMIC} == .true. ]]; then
        ln -sf ${FV3_IC}/../ExtData .
    else
        ln -sf  @[INPUTDATA_ROOT]/GOCART/p8c_5d/ExtData .
    fi
fi

#merra2
if [ $IAER = 1011 ]; then
    for n in 01 02 03 04 05 06 07 08 09 10 11 12; do
        cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2_y14_24/merra2_1423_${n}.nc aeroclim.m${n}.nc
    done
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat  optics_BC.dat
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_OC.v1_3.dat  optics_OC.dat
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_DU.v15_3.dat optics_DU.dat
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SS.v3_3.dat  optics_SS.dat
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SU.v1_3.dat  optics_SU.dat
fi

#rad_c_gocart
if [ $IAER = 2011 ]; then
    for n in 01 02 03 04 05 06 07 08 09 10 11 12; do
        cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/MERRA2_y14_24/merra2_1423_${n}.nc aeroclim.m${n}.nc
    done
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_BC.v1_3.dat  optics_BC.dat
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_OC.v1_3.dat  optics_OC.dat
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_DU.v15_3.dat optics_DU.dat
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SS.v3_3.dat  optics_SS.dat
    cp @[INPUTDATA_ROOT]/FV3_input_data_INCCN_aeroclim/aer_data/LUTS/optics_SU.v1_3.dat  optics_SU.dat

    if [[ ${BMIC} == .true. ]]; then
        DIR_OPT=./ExtData/monochromatic
        cp ${DIR_OPT}/optics_BC.v1_3.nc  optics_BC.nc
        cp ${DIR_OPT}/optics_OC.v1_3.nc  optics_OC.nc
        cp ${DIR_OPT}/optics_DU.v15_3.nc optics_DU.nc
        cp ${DIR_OPT}/optics_SS.v3_3.nc  optics_SS.nc
        cp ${DIR_OPT}/optics_SU.v1_3.nc  optics_SU.nc
        cp ${DIR_OPT}/optics_BRC.v1_5.nc  optics_BRC.nc
        cp ${DIR_OPT}/optics_NI.v2_5.nc  optics_NI.nc
    fi
fi

if [ $GWD_OPT -ne 0 ]; then
    cp @[INPUTDATA_ROOT]/FV3_input_data/ugwp_c384_tau.nc ./ugwp_limb_tau.nc
    if [[ $GFSv17opn == .true. ]]; then
        cp @[INPUTDATA_GFSv17opn]/FV3_fix/oro_data_ls* ./INPUT
        cp @[INPUTDATA_GFSv17opn]/FV3_fix/oro_data_ss* ./INPUT
    else
        cp @[INPUTDATA_ROOT]/${FV3_DIR}/INPUT_L127_gfsv17/oro_data_ls* ./INPUT
        cp @[INPUTDATA_ROOT]/${FV3_DIR}/INPUT_L127_gfsv17/oro_data_ss* ./INPUT
    fi
fi

if [ $IMP_PHYSICS = 8 ]; then
    cp @[INPUTDATA_ROOT]/FV3_fix/CCN_ACTIVATE.BIN CCN_ACTIVATE.BIN
    cp @[INPUTDATA_ROOT]/FV3_fix/freezeH2O.dat freezeH2O.dat
    cp @[INPUTDATA_ROOT]/FV3_fix/qr_acr_qgV2.dat qr_acr_qgV2.dat
    cp @[INPUTDATA_ROOT]/FV3_fix/qr_acr_qsV2.dat qr_acr_qsV2.dat
fi